Spatial light heterogeneity within forest canopies drives organ-level competition and whole-plant functioning, yet how shade-induced lower-canopy senescence and retention affect upper-canopy photosynthesis in marcescent species remains unclear. In this study, three-year-old Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] seedlings were subjected to half-canopy (moderate shading, T1) and three-quarter canopy (severe shading, T2) treatments, alongside a non-shaded control (CK), to investigate the monthly and diurnal dynamics of intra-canopy photosynthetic and photochemical traits. The results showed that long-term shading significantly reduced lower-needle photosynthetic capacity and accelerated senescence, as limitations shifted from stomatal (during January–April) to non-stomatal (during May–June), ultimately impairing photosystem II (PSII) (indicated by a significant decline in F_v/F_m) and inducing needle retention. Concurrently, upper needles exhibited pronounced non-autonomous responses with the net photosynthetic rate (P_n), stomatal conductance (G_s), and water-use efficiency (WUE) decreasing with increasing shading intensity. Compared with the CK, the reduction in P_n reached 61.99% under severe shading (T2). Shading weakened the strong positive coupling between the upper and lower canopies observed in the control (r = 0.615 to 0.978), shifting specific parameters to an antagonistic relationship under T2 (e.g., lower-canopy P_n and upper-canopy L_s, r = −0.897), which indicates a transition from integrated coordination to functional differentiation. Chlorophyll fluorescence correlations further revealed that while moderate shading (T1) maintained PSII photochemical stability, severe shading (T2) induced divergent energy allocation, with lower-canopy F_v/F_m negatively associated with upper-canopy qP and NPQ (r = −0.361 and −0.355, p < 0.05). Furthermore, lower-canopy senescence exerted a 1–2-month time-lagged effect on upper-canopy photosynthesis, with gas exchange parameters demonstrating greater sensitivity than photochemical processes. Overall, the results from three-year-old potted seedlings suggest that shade-induced lower-canopy needle senescence and retention may regulate upper-canopy photosynthetic function, driving an intra-canopy transition from coordination to decoupling and antagonism through distinct time-lagged effects. Further field studies are needed to determine whether these patterns occur in mature C. lanceolata stands and how they influence plantation productivity and marcescence dynamics.